Table 2.
Summary of major candidate genes related to meat quality characteristics and feed intake in Sanga cattle population detected by XP-EHH and XP-CLR statistics (see Additional file 1: Table S1 and Additional file 2: Table S2)
| Candidate genes | Chr. | Window (Mbp) | XP-CLR | Max XP-EHH | XP-EHH P-value | Tajima’s D | Weighted FST | Species, trait and reference |
|---|---|---|---|---|---|---|---|---|
| PIK3CB | 1 | 131.50–131.55 | 121.48 | 2.21 | 1.69.E-03 | −1.06 | 0.27 | RFI [79]a |
| MRAS | 1 | 131.73–131.78 | 112.25 | - | - | −1.87 | 0.16 | FCE [79]a |
| PLA2G2A | 2 | 133.28–133.33 | 117.48 | - | - | 0.70 | 0.27 | IMF [58]b, [59]c |
| CAPZB | 2 | 133.78–133.83 | 142.50 | - | - | −0.47 | 0.22 | Tenderness [32]c |
| COL9A2 | 3 | 106.38–106.43 | 107.14 | 1.93 | 5.95.E-03 | −1.30 | 0.15 | Tenderness [46]b |
| LIMA | 5 | 29.78–29.83 | 117.18 | - | - | −0.33 | 0.39 | Tenderness [45]b |
| SLC48A1 | 5 | 32.63–32.68 | 101.45 | 1.80 | 6.96.E-03 | −0.35 | 0.26 | Meat color [68]d |
| MB | 5 | 74.18–74.23 | 129.86 | 1.96 | 5.00.E-03 | −0.98 | 0.20 | Meat color [41, 67]d |
| APOL6 | 5 | 74.20–74.25 | - | 2.00 | 5.00.E-03 | −0.91 | 0.13 | IMF [65]d |
| ATP8A1 | 6 | 62.90–62.95 | 264.27 | 2.02 | 4.00.E-03 | −1.39 | 0.36 | FCE [76]c |
| PDGFRA | 6 | 71.35–71.40 | 408.60 | 2.61 | 3.00.E-04 | −2.29 | 0.45 | Tenderness [53]b |
| MAP3K5 | 9 | 75.55–75.60 | 147.37 | 2.09 | 3.00.E-03 | −0.23 | 0.15 | RFI [75]b |
| PARK2 | 9 | 99.13–99.18 | 132.40 | 2.34 | 2.36.E-03 | −0.27 | 0.30 | IMF [62]a |
| PKM2 | 10 | 18.95–19.00 | - | 1.97 | 2.00.E-03 | −1.18 | 0.25 | Tenderness [32]d, [52]a; IMF [64]b; Drip loss [70, 71]b |
| ZNF410 | 10 | 85.68–85.73 | 165.86 | 2.18 | 1.94.E-03 | −0.67 | 0.28 | Tenderness [32]c, [35]b |
| AHSA1 | 10 | 89.70–89.75 | - | 2.23 | 2.00.E-03 | −1.47 | 0.31 | IMF [66]c |
| MAP4K4 | 11 | 6.65–6.70 | - | 1.85 | 9.00.E-03 | 0.72 | 0.08 | Drip loss [70, 71]b |
| NFATC2 | 13 | 80.00–80.05 | - | 2.01 | 4.24.E-03 | 2.53 | 0.25 | Tenderness [55]d |
| WWP1 | 14 | 78.63–78.68 | 133.90 | - | - | 1.03 | 0.18 | Tenderness [50]d |
| OR2D2, OR10A4, OR2D3 | 15 | 46.40–46.45 | - | 2.07 | 3.45.E-03 | 2.61 | 0.18 | Feed intake [78]d; [77]b |
| MAP2K3 | 19 | 35.85–35.90 | - | 1.93 | 4.00.E-03 | −0.20 | 0.16 | IMF [49]b |
| PLCD3 | 19 | 45.40–45.45 | - | 1.89 | 5.00.E-03 | −0.18 | 0.03 | IMF [56]d |
| TIMP2 | 19 | 54.10–54.15 | - | 1.88 | 7.46.E-03 | −0.73 | 0.18 | RFI [73]c |
| PLCD1 | 22 | 11.45–11.50 | 195.30 | 2.12 | 3.00.E-03 | −1.43 | 0.14 | IMF [56]d |
| ROCK1 | 24 | 35.48–35.53 | 130.40 | 2.22 | 1.61.E-03 | 0.93 | 0.29 | Tenderness [48]a; IMF [61]b |
| PRKG1 | 26 | 7.43–7.48 | 166.61 | - | - | −1.27 | 0.13 | Tenderness [54]d; IMF [36]b; RFI [72]c |
Note: Chr. Chromosome, Window: start and end positions of the gene region; RFI residual feed intake, FCE feed conversion efficiency, IMF intramuscular fat; Superscripts in the Species, Trait and Reference column indicate the species that the trait has been previously reported for as achicken, bpork, cbeef, dgeneral (not for a specific species)